SRPRA

SRP receptor subunit alpha

Basic information

Region (hg38): 11:126262937-126269144

Previous symbols: [ "SRPR" ]

Links

ENSG00000182934 ∙ NCBI:6734 ∙ OMIM:182180 ∙ HGNC:11307 ∙ Uniprot:P08240 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRPRA gene.

• not provided (8 variants)
• Inborn genetic diseases (4 variants)
• SRPRA-related condition (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRPRA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					1	1
Total	0	0	9	3	2

Variants in SRPRA

This is a list of pathogenic ClinVar variants found in the SRPRA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-126265036-C-T		SRPRA-related disorder	Benign (Jul 01, 2022)
11-126265065-A-C		not specified	Uncertain significance (Jul 20, 2021)
11-126265094-G-C		Shwachman-Diamond syndrome 1;Severe congenital neutropenia	Pathogenic (Jan 06, 2020)
11-126265108-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-126265112-G-C			Uncertain significance (Sep 01, 2023)
11-126265132-A-G			Uncertain significance (Aug 01, 2023)
11-126265173-C-T		See cases	Uncertain significance (Apr 10, 2022)
11-126265319-G-A			Likely benign (Feb 01, 2023)
11-126266516-T-C		not specified	Uncertain significance (Nov 09, 2021)
11-126266580-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-126266778-C-T			Uncertain significance (Sep 28, 2021)
11-126267540-GTC-G		SRPRA-related disorder	Likely benign (Sep 25, 2020)
11-126267605-AGCACTT-A		SRPRA-related disorder	Uncertain significance (Apr 21, 2023)
11-126267674-G-A			Likely benign (Jan 01, 2023)
11-126268072-G-C		not specified	Uncertain significance (Jul 09, 2021)
11-126268727-G-A		SRPRA-related disorder	Likely benign (Jun 17, 2021)
11-126268751-G-A			Likely benign (Oct 01, 2022)
11-126268860-G-A			Benign (Jun 28, 2018)
11-126269044-G-C		Mitochondrial complex I deficiency, nuclear type 1	Conflicting classifications of pathogenicity (Aug 22, 2020)
11-126269056-C-A		Mitochondrial complex I deficiency, nuclear type 1	Uncertain significance (Jan 13, 2018)
11-126269114-C-G			Likely benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRPRA	protein_coding	protein_coding	ENST00000332118	14	6226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.778	0.222	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	329	394	0.835	0.0000236	4194
Missense in Polyphen		125	183.72	0.68039		1923
Synonymous	-0.681	151	141	1.07	0.00000766	1271
Loss of Function	3.92	5	27.0	0.185	0.00000121	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000884	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the SRP (signal recognition particle) receptor. Ensures, in conjunction with the signal recognition particle, the correct targeting of the nascent secretory proteins to the endoplasmic reticulum membrane system.
• Pathway: Protein export - Homo sapiens (human);XBP1(S) activates chaperone genes;SRP-dependent cotranslational protein targeting to membrane;Translation;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.43

Haploinsufficiency Scores

• pHI: 0.638
• hipred: Y
• hipred_score: 0.711
• ghis: 0.574

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Srpr

Gene ontology

• Biological process: protein targeting;cotranslational protein targeting to membrane;SRP-dependent cotranslational protein targeting to membrane;IRE1-mediated unfolded protein response;protein targeting to ER
• Cellular component: signal recognition particle receptor complex;endoplasmic reticulum membrane;membrane;extracellular exosome
• Molecular function: RNA binding;GTPase activity;signal recognition particle binding;GTP binding